Small RNA control of denitrification and N2O emissions in bacteria

Moeller, Sophie Louise (2023) Small RNA control of denitrification and N2O emissions in bacteria. Doctoral thesis, University of East Anglia.

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Abstract

Anthropogenic influences have led to a shift in the nitrogen cycle resulting in an increase in microbial emissions of the potent greenhouse gas nitrous oxide (N2O) into the atmosphere. As the genetic, physiological, and environmental factors regulating the microbial processes responsible for the production and consumption of N2O are not fully understood, this represents a critical knowledge gap in the development of future mitigation strategies. Non-coding small RNAs (sRNAs) regulate a wide range of physiological processes in microorganisms that allow them to rapidly respond to changes in environmental conditions. These have predominantly been studied in a limited number of model organisms but with improvements in the techniques for sRNA discovery it is becoming increasingly clear that sRNAs play a crucial role in environmentally relevant pathways as well. For example, several sRNAs have been shown to control important enzymatic processes within the nitrogen cycle and many more have been identified in model nitrogen cycling organisms such as the model denitrifier Paracoccus denitrificans.

The discovery of the sRNA DenR has demonstrated the influence of a single sRNA on the denitrification pathway through interaction with a novel GntR-type regulator NirR, which in turn stalls denitrification at the stage of nitrite reduction. This study aims to further explore the role of this novel regulatory mechanism within the denitrification regulatory network. Furthermore, this thesis presents information on how to further unravel the sRNA regulatory network in the model organism P. denitrificans and show indications for the involvement of further sRNAs as well as the involvement of the RNA chaperone Hfq. To address knowledge gaps regarding the transcriptome during denitrification conditions, a global transcription start site analysis is presented which provides a solid foundation for further research into the role of sigma factors and promoter activity during complete and incomplete denitrification. Together these investigations highlight the importance of P. denitrificans as a biochemical and physiological model for denitrification to identify potential novel targets for mitigation strategies and combat climate change.

Item Type:	Thesis (Doctoral)
Faculty \ School:	Faculty of Science > School of Biological Sciences
Depositing User:	Nicola Veasy
Date Deposited:	02 Jul 2024 08:04
Last Modified:	02 Jul 2024 08:04
URI:	https://ueaeprints.uea.ac.uk/id/eprint/95729
DOI:

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